Reducing HIV-1 env gene CpG frequency increases the replication capacity of the HXB2 virus strain

Synonymous replacement of CpG dinucleotides in the HIV-1 envelope (env) coding region has been correlated with evasion of the antiviral activity of the zinc-finger antiviral protein (ZAP). We aimed to explore the effect of depleting HIV-1 env CpG dinucleotides by synonymous substitution on ex vivo viral replication capacity. To this end, we eliminated 11 env CpG dinucleotides through synonymous substitutions in the CXCR4-tropic HXB2 strain. The replication kinetics in MT-4 cells and peripheral blood mononuclear cells (PBMCs) of the WT and synonymously recoded mutant viruses were indistinguishable. However, virus competition assays in MT4 cells between the WT and recoded viruses showed that the mutant with fewer CpG dinucleotides quickly overgrew the WT virus. These results demonstrate that a reduction in HIV-1 env CpG dinucleotide frequency can improve viral replication capacity in cell culture. Our results support the previous observation that the frequency of CpGs in the HIV-1 env region correlates with differences in clinical progression rates in infected individuals.